Computational Biologist

Key Skills

Java Programming, Python Programming, C++, C Programming, SQL, Cloud computing, Scala Programming, Machine learning techniques, Data science techniques, MATLAB Programming, PyTorch, TensorFlow, R Programming

Job Description

Calico is a research and development company whose mission is to harness advanced technologies to increase our understanding of the biology that controls lifespan and healthspan, and to devise interventions that enable people to lead longer and healthier lives. Executing on this mission will require an unprecedented level of interdisciplinary effort and a long-term focus for which funding is already in place.

Position description:

Calico is seeking a computational biologist to join a team of scientists investigating aging and age-related diseases using genetics and functional genomics in humans and a diversity of model systems.

Genomics offers rich, informative profiles of organism state during aging. We collect these data to build causal models for organism state, that reveal the critical underlying cellular processes and more readily highlight promising intervention points. The ideal candidate is passionate about working to better understand how genomes work and their role in propagating the harmful changes that occur during aging.

Predictive modeling with cutting edge machine learning tools are at the core of this work, exemplified by recent publications modeling regulatory activity as a function of DNA sequence using deep learning.

• Avsec, ?. et al.Effective gene expression prediction from sequence by integrating long-range interactions. Nat Methods18, 1196–1203 (2021).
• Yuan, H. & Kelley, D. R. scBasset: Sequence-based modeling of single cell ATAC-seq using convolutional neural networks. bioRxiv09.08.459495 (2021).
• Agarwal, V. & Kelley, D. The genetic and biochemical determinants of mRNA degradation rates in mammals. bioRxiv03.18.484474 (2022).

Additional research on single cell genomics in aging can be found here,

This work benefits from world-class computing infrastructure and continued collaboration with top machine learning researchers within Alphabet.

Position responsibilities:

• Develop novel machine learning approaches for biological sequence analysis towards predicting genetic variant effects and fine-mapping aging-related disease associations.
• Interact closely with experimental biologists to understand and analyze large-scale datasets to reach biological conclusions that inform Calico’s pursuit.
• Communicate research via publications, presentations, web interfaces, and open software.

Position requirements:

• PhD in computational biology, bioinformatics, computer science, or a related discipline.
• Strong computational fundamentals including machine learning, algorithms, and data structures.
• Strong biological knowledge and interest; familiarity with biological data resources.
• Fluent coding in preferably Python but at least one common bioinformatics programming language.
• Experience analyzing genomics experiments (e.g. RNA-seq, ATAC-seq, ChIP-seq, scRNA-seq).
• Experience applying machine learning to biological problems.
• Intellectual curiosity, attention to detail, consistent follow-through, proactive approach to collaborations, demonstrated ability to work in a team environment.

Calico requires all new hires to be fully vaccinated for COVID-19 prior to the first date of employment. As required by applicable law, Calico will consider requests for Reasonable Accommodations.